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Changes to buildnml to permit use of new dglc component with ctms #71

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Commits on Nov 28, 2023

  1. Add an LII test using the spunup 1850 ne30pg3_g17 file

    (cherry picked from commit d6994f7)
    ekluzek committed Nov 28, 2023
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  2. Adjust tests with tests expected to pass

    (cherry picked from commit 9882289)
    ekluzek committed Nov 28, 2023
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  4. Merge pull request ESCOMP#2240 from samsrabin/use-basetlatvary-params

    Use baset_latvary parameters
    
    Namelist parameters baset_latvary_slope and baset_latvary_intercept were never actually used, with values of 0.4 and 12 being hard-coded in the relevant subroutine instead. This PR fixes that, and also adds unit testing of a refactored function that uses them.
    samsrabin authored Nov 28, 2023
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  5. Fix some of the filepaths

    (cherry picked from commit a4eff78)
    
     Conflicts:
    	bld/namelist_files/namelist_defaults_ctsm.xml
    ekluzek committed Nov 28, 2023
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  6. Add issue number to expected fails

    (cherry picked from commit 4e09130)
    
     Conflicts:
    	cime_config/testdefs/ExpectedTestFails.xml
    ekluzek committed Nov 28, 2023
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  7. Update baseline directory for Derecho

    (cherry picked from commit b916d38)
    ekluzek committed Nov 28, 2023
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  8. Change queue and wallclock limit for Derecho

    (cherry picked from commit 863ed22)
    ekluzek committed Nov 28, 2023
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  9. Add 2000 and HIST tests for ne30np4.pg3 to cesm3_dev testlist, remove…

    … the PEM test that is no longer needed and doesn't have a testmod for it
    
    (cherry picked from commit 04853a8)
    ekluzek committed Nov 28, 2023
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  10. Get finidat file working for 2000 ne30np4.pg3 clm5_1_cam6.0 working

    (cherry picked from commit 88ac3ae)
    ekluzek committed Nov 28, 2023
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  11. Update ne30np4.pg3 1850 finidat file so LII tests work, and add in ne…

    …30np4.pg3 landuse.timeseries file
    
    (cherry picked from commit d3a82a5)
    
     Conflicts:
    	bld/namelist_files/namelist_defaults_ctsm.xml
    ekluzek committed Nov 28, 2023
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  12. Actually turn Meier off

    (cherry picked from commit 1a09d07)
    
     Conflicts:
    	cime_config/testdefs/testmods_dirs/clm/ciso_decStartNoMeier/user_nl_clm
    ekluzek committed Nov 28, 2023
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  16. Merge tag 'ctsm5.1.dev155' into derecho1

    Use baset_latvary parameters
    
    Namelist parameters baset_latvary_slope and baset_latvary_intercept were never actually used, with values of 0.4 and 12 being hard-coded in the relevant subroutine instead. This PR fixes that, and also adds unit testing of a refactored function that uses them.
    ekluzek committed Nov 28, 2023
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  17. The ne30pg3 finidat file needs to do interpolation to get started sin…

    …ce it was created with ctsm5.2 datasets
    ekluzek committed Nov 28, 2023
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  18. move add_cime_to_path import

    adrifoster committed Nov 28, 2023
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  19. Remove the ne30pg3 LII tests because they will fail as use_init_inter…

    …p is required because the finidat file is based on ctsm5.2 datasets
    ekluzek committed Nov 28, 2023
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  20. Add use_init_interp to the ne30pg3 finidat file, because it's needed …

    …for non ctsm5.2 surface datasets
    ekluzek committed Nov 28, 2023
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Commits on Nov 29, 2023

  1. Lengthen test time

    ekluzek committed Nov 29, 2023
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  4. Merge tag 'ctsm5.1.dev155' into fates-luh2

    Use baset_latvary parameters
    
    Namelist parameters baset_latvary_slope and baset_latvary_intercept were never actually used, with values of 0.4 and 12 being hard-coded in the relevant subroutine instead. This PR fixes that, and also adds unit testing of a refactored function that uses them.
    glemieux committed Nov 29, 2023
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Commits on Nov 30, 2023

  1. fates external pointer

    rgknox committed Nov 30, 2023
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  2. merge up to dev155

    rgknox committed Nov 30, 2023
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  4. First pass at adding derecho tests, also change the syntax for ones w…

    …ith options per machine to options after machine lists, and add intel-oneapi and nvhpc tests to test lists with clm_short
    ekluzek committed Nov 30, 2023
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  12. Merge pull request ESCOMP#2273 from samsrabin/disable-meier-roughness

    Do not use Meier roughness by default, even with 5.1
    
    ctsm5.1.dev155 had turned on Meier2022 surface roughness calculation by default for 5.1 compsets. Several bugs have recently emerged that were not caught by pre-merge testing, so this tag reverts that change. Thus, the ZengWang2007 method is default for all compsets again.
    samsrabin authored Nov 30, 2023
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  13. add luh2 testmod

    glemieux committed Nov 30, 2023
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  16. Fix comment alignment

    slevis-lmwg committed Nov 30, 2023
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Commits on Dec 1, 2023

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  3. Fix pe-layouts for Derecho, remove new nvhpc tests on Derecho that we…

    …ren't in Cheyenne, and remove the intel-oneapi tests since they fail
    ekluzek committed Dec 1, 2023
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  4. Merge tag 'ctsm5.1.dev156' into derecho1

    Do not use Meier roughness by default, even with 5.1
    
    ctsm5.1.dev155 had turned on Meier2022 surface roughness calculation by default for 5.1 compsets. Several bugs have recently emerged that were not caught by pre-merge testing, so this tag reverts that change. Thus, the ZengWang2007 method is default for all compsets again.
    ekluzek committed Dec 1, 2023
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  5. Correct expected fail

    ekluzek committed Dec 1, 2023
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  8. Remove two nvhpc tests that fail, one from Cheyenne that wasn't there…

    … before and the other from Derecho
    ekluzek committed Dec 1, 2023
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  13. Add NEON tests to Derecho

    ekluzek committed Dec 1, 2023
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Commits on Dec 2, 2023

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Commits on Dec 3, 2023

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Commits on Dec 4, 2023

  1. Remove references to Cheyenne and make it more explicit what to do on…

    … different systems, as well as adding Derecho
    ekluzek committed Dec 4, 2023
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  2. Update /glade/p references

    ekluzek committed Dec 4, 2023
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  4. Update /glade/p paths

    ekluzek committed Dec 4, 2023
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  5. First stab at getting the test/tools framework to work on Derecho, is…

    …n't working as conda and module is not available in my default shell
    ekluzek committed Dec 4, 2023
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  8. Merge tag 'ctsm5.1.dev156' into externals-for-derecho

    Do not use Meier roughness by default, even with 5.1
    
    ctsm5.1.dev155 had turned on Meier2022 surface roughness calculation by default for 5.1 compsets. Several bugs have recently emerged that were not caught by pre-merge testing, so this tag reverts that change. Thus, the ZengWang2007 method is default for all compsets again.
    samsrabin committed Dec 4, 2023
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Commits on Dec 5, 2023

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  2. Merge pull request ESCOMP#2270 from samsrabin/externals-for-derecho

    Update Externals.cfg to work on Derecho
    samsrabin authored Dec 5, 2023
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  3. Merge tag 'ctsm5.1.dev157' into derecho1

    Update Externals.cfg to work on Derecho
    ekluzek committed Dec 5, 2023
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Commits on Dec 6, 2023

  1. Merge tag 'ctsm5.1.dev155' into bugfix_iss2264

    Use baset_latvary parameters
    
    Namelist parameters baset_latvary_slope and baset_latvary_intercept were never actually used, with values of 0.4 and 12 being hard-coded in the relevant subroutine instead. This PR fixes that, and also adds unit testing of a refactored function that uses them.
    slevis-lmwg committed Dec 6, 2023
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  3. Run through black

    ekluzek committed Dec 6, 2023
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  4. ignore black format

    ekluzek committed Dec 6, 2023
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  6. Restore perl CLMBuildNamelist back to ctsm5.1.dev157 version, the ne3…

    …0np4.pg3 work around isn't needed, this fixes ESCOMP#2268
    ekluzek committed Dec 6, 2023
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Commits on Dec 7, 2023

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  4. Fix testname

    ekluzek committed Dec 7, 2023
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Commits on Dec 8, 2023

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  3. Merge remote-tracking branch 'adrifoster/run_neon-cime_path_bug' into…

    … subset_data_fix
    
    Resolved conflicts:
    python/ctsm/site_and_regional/run_neon.py
    slevis-lmwg committed Dec 8, 2023
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  9. Update Change files

    ekluzek committed Dec 8, 2023
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  10. Update changelog

    ekluzek committed Dec 8, 2023
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  11. Merge pull request ESCOMP#2269 from ekluzek/derecho1

    First tag with PE layouts and testing for Derecho
    ekluzek authored Dec 8, 2023
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  12. Merge remote-tracking branch 'escomp/master' into subset_data_fix

    Resolved conflicts:
    .git-blame-ignore-revs
    slevis-lmwg committed Dec 8, 2023
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  14. Minor reformat

    slevis-lmwg committed Dec 8, 2023
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  15. Revert "Minor reformat"

    This reverts commit bb536ed.
    First of 3 expected reverts.
    slevis-lmwg committed Dec 8, 2023
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  16. Revert "Add module load cdo to regrid_ggcmi_shdates.py for sys test t…

    …o pass"
    
    This reverts commit ff02bad.
    Second of 3 expected reverts.
    slevis-lmwg committed Dec 8, 2023
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  17. Revert "Merge remote-tracking branch 'samsrabin/regrid-shdate-dev' in…

    …to subset_data_fix"
    
    This reverts commit f47de1d, reversing
    changes made to f335221.
    
    Resolve conflicts:
    .git-blame-ignore-revs
    slevis-lmwg committed Dec 8, 2023
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Commits on Dec 9, 2023

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Commits on Dec 11, 2023

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  2. fix pes

    mvdebolskiy committed Dec 11, 2023
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  3. Fates pointer

    rgknox committed Dec 11, 2023
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Commits on Dec 12, 2023

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  2. Merge pull request ESCOMP#2253 from slevis-lmwg/subset_data_fix

    Various BFB fixes and updates.
    slevis-lmwg authored Dec 12, 2023
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Commits on Dec 13, 2023

  1. Merge tag 'ctsm5.1.dev159' into fates-luh2

    Various BFB fixes and updates
    
    Purpose/description of changes
    ------------------------------
    the default comes in a later tag (slevis)
    
    Regular and python testing passed.
    
    Does not change answers relative to dev158.
    glemieux committed Dec 13, 2023
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Commits on Dec 14, 2023

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  2. update external

    rgknox committed Dec 14, 2023
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  3. Revert "Revert "Merge remote-tracking branch 'samsrabin/regrid-shdate…

    …-dev' into subset_data_fix""
    
    This reverts commit a059445.
    samsrabin committed Dec 14, 2023
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  6. Rename TestRegridGgcmiShdates to TestUtilsImportCoord.

    Similarly rename its file.
    samsrabin committed Dec 14, 2023
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Commits on Dec 15, 2023

  1. Update the default fates paramfile

    A newer parameter file was generated that reduces the maximum
    number of fates patches for the default configuration.  This
    avoids misalignment between the default surface datasets.
    glemieux committed Dec 15, 2023
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  2. Pass surfpft bounds as input argumment

    The wt_nat_patch array is allocated using surfpft bounds.  While
    surfpft and natpft will typically match, this isn't the case
    for fates currently.  As such the nag compiler will complain
    if the input array has lower bounds for its dimensions than
    the dummy argument bounds.
    glemieux committed Dec 15, 2023
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Commits on Dec 17, 2023

  1. Delete a print(lat).

    samsrabin committed Dec 17, 2023
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  3. chdir out of tempdir in tests and regrid_ggcmi_shdates.

    Resolves ESCOMP#2167. Affected scripts:
    * test_sys_mesh_modifier
    * test_sys_run_neon
    * regrid_ggcmi_shdates
    samsrabin committed Dec 17, 2023
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Commits on Dec 18, 2023

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  6. Remove an extraneous #.

    samsrabin committed Dec 18, 2023
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  7. Reformatting with black.

    samsrabin committed Dec 18, 2023
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  9. Merge tag 'ctsm5.1.dev159' into cropresidues3-dev

    Various BFB fixes and updates
    
    Purpose/description of changes
    ------------------------------
    the default comes in a later tag (slevis)
    
    Regular and python testing passed.
    
    Does not change answers relative to dev158.
    samsrabin committed Dec 18, 2023
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Commits on Dec 19, 2023

  1. update changelog

    glemieux committed Dec 19, 2023
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  2. externals

    rgknox committed Dec 19, 2023
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Commits on Dec 20, 2023

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  2. Updated call to fates history

    rgknox committed Dec 20, 2023
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Commits on Dec 27, 2023

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Commits on Dec 29, 2023

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  4. Merge tag 'ctsm5.1.dev159' into tillage

    Various BFB fixes and updates
    
    Purpose/description of changes
    ------------------------------
    the default comes in a later tag (slevis)
    
    Regular and python testing passed.
    
    Does not change answers relative to dev158.
    samsrabin committed Dec 29, 2023
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  5. Typo fix in crop Tech Note.

    samsrabin committed Dec 29, 2023
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  8. Add 'till' testdef.

    samsrabin committed Dec 29, 2023
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Commits on Dec 31, 2023

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  2. Only get a default luh timeseries file if you need one, and ask for o…

    …ne at the model resolution and sim_year_range
    ekluzek committed Dec 31, 2023
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  4. Update change files

    ekluzek committed Dec 31, 2023
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  5. Merge pull request ESCOMP#2076 from glemieux/fates-luh2

    Add FATES land use change module to pass LUH2 data to FATES
    ekluzek authored Dec 31, 2023
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Commits on Jan 3, 2024

  1. Merge tag 'ctsm5.1.dev160' into refactor-crop-gdd-runmeans

    FATES landuse version 1
    
    This tag enables FATES to utilize the state and transitions data
    from the Land Use Harmonization (https://luh.umd.edu/) data sets.
    This data has been preprocessed using tooling provided by FATES via
    a separate pull request (FATES#1032).  A new module has been added
    to the dyn_subgrid directory that largely adapts the dynHarvest
    module to import and read this minimially processed data, which is
    data is passed to fates.
    samsrabin committed Jan 3, 2024
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Commits on Jan 4, 2024

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  2. Merge pull request ESCOMP#2060 from samsrabin/refactor-crop-gdd-runmeans

    Refactor 20-year running means of crop GDD accumulation
    
    Three variables track the 20-year running mean of GDD accumulation (base temperatures 0, 8, and 10°C) during the "growing season" (April through September in the Northern Hemisphere, October through March in the Southern Hemisphere). This update refactors those to use accumulMod, resolving overly-strong weighting of the first few years after a crop becomes active.
    samsrabin authored Jan 4, 2024
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Commits on Jan 5, 2024

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  4. Merge tag 'ctsm5.1.dev161' into regrid-shdate-dev2

    Refactor 20-year running means of crop GDD accumulation
    
    Three variables track the 20-year running mean of GDD accumulation (base temperatures 0, 8, and 10°C) during the "growing season" (April through September in the Northern Hemisphere, October through March in the Southern Hemisphere). This update refactors those to use accumulMod, resolving overly-strong weighting of the first few years after a crop becomes active.
    samsrabin committed Jan 5, 2024
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  6. Merge pull request ESCOMP#2292 from samsrabin/regrid-shdate-dev2

    Improvements to processing of crop calendar files (v2)
    
    In python/ctsm/crop_calendars/, process_ggcmi_shdates.py and regrid_ggcmi_shdates.py are used to convert the raw GGCMI crop calendar files into CTSM-compatible versions. This update fixes some bugs, removes dependencies on the nco utilities, enables the use of surface datasets as template files (in addition to the existing ability to use CTSM output files), and standardizes things for consistency with other CTSM Python tools.
    samsrabin authored Jan 5, 2024
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  7. Merge tag 'ctsm5.1.dev162' into cropresidues3

    Improvements to processing of crop calendar files
    
    In python/ctsm/crop_calendars/, process_ggcmi_shdates.py and regrid_ggcmi_shdates.py are used to convert the raw GGCMI crop calendar files into CTSM-compatible versions. This update fixes some bugs, removes dependencies on the nco utilities, enables the use of surface datasets as template files (in addition to the existing ability to use CTSM output files), and standardizes things for consistency with other CTSM Python tools.
    samsrabin committed Jan 5, 2024
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Commits on Jan 8, 2024

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  4. Formatting with black.

    samsrabin committed Jan 8, 2024
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Commits on Jan 10, 2024

  1. Added fates two-stream test

    rgknox committed Jan 10, 2024
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  4. Add NEON tests to expected fail list.

    See ESCOMP#2310: NEON tests sometimes fail (ESCOMP#2310)
    samsrabin committed Jan 10, 2024
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  5. NEON tests can also fail during RUN.

    See ESCOMP#2310: NEON tests sometimes fail (ESCOMP#2310)
    samsrabin committed Jan 10, 2024
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  6. Enable tillage in two aux_clm tests.

    (cherry picked from commit 142c2c1)
    samsrabin committed Jan 10, 2024
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  8. Add residue removal test.

    samsrabin committed Jan 10, 2024
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  11. Merge branch 'tillage' into tillage-and-residues4

    Makes no changes, but I realized the cherry-pick I did before won't let Github recognize that this is up-to-date with the tillage branch.
    samsrabin committed Jan 10, 2024
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  14. Merge pull request ESCOMP#2311 from samsrabin/tillage-and-residues4

    Adds capability for cropland soil tillage and post-harvest residue removal.
    
    Tillage: This PR brings in the tillage code written by Sam Levis and Michael Graham and used in Graham et al. (2021, ERL, doi:10.1088/1748-9326/abe6c6). Low- and high-intensity tillage here work by increasing the decomposition rate of different soil carbon pools. These "decomposition multipliers" vary based on soil pool and how long it's been since the crop was planted; they are set with new paramfile variables till_decompk_multipliers and mimics_till_decompk_multipliers. Note that tillage is off by default.
    
    Residue removal: Adds a parameter hat represents what fraction of post-harvest crop residues (stems and leaves) should be removed to the crop product pool rather than being transferred to litter.
    samsrabin authored Jan 10, 2024
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  15. Merge tag 'ctsm5.1.dev163' into fates-two-stream-dev163

    Adds capability for cropland soil tillage and post-harvest residue removal.
    
    Tillage: This PR brings in the tillage code written by Sam Levis and Michael Graham and used in Graham et al. (2021, ERL, doi:10.1088/1748-9326/abe6c6). Low- and high-intensity tillage here work by increasing the decomposition rate of different soil carbon pools. These "decomposition multipliers" vary based on soil pool and how long it's been since the crop was planted; they are set with new paramfile variables till_decompk_multipliers and mimics_till_decompk_multipliers. Note that tillage is off by default.
    
    Residue removal: Adds a parameter hat represents what fraction of post-harvest crop residues (stems and leaves) should be removed to the crop product pool rather than being transferred to litter.
    rgknox committed Jan 10, 2024
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  17. Added two-stream nocomp test

    rgknox committed Jan 10, 2024
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Commits on Jan 11, 2024

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  2. black/pylint

    TeaganKing committed Jan 11, 2024
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Commits on Jan 12, 2024

  1. mostly testing updates

    TeaganKing committed Jan 12, 2024
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Commits on Jan 16, 2024

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  2. rename arg_parse

    TeaganKing committed Jan 16, 2024
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  3. black arg_parse unit test

    TeaganKing committed Jan 16, 2024
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  6. update change logs

    rgknox committed Jan 16, 2024
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Commits on Jan 17, 2024

  1. Update change files

    ekluzek committed Jan 17, 2024
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  2. Merge pull request ESCOMP#2265 from rgknox/fates-two-stream

    Fates two stream API
    ekluzek authored Jan 17, 2024
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Commits on Jan 20, 2024

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  2. Merge pull request ESCOMP#2323 from slevis-lmwg/merge_tag_meier_and_p…

    …r2212
    
    Merge tag: Turn on Meier2022, tillage, residue removal; bring in ESCOMP#2212
    slevis-lmwg authored Jan 20, 2024
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Commits on Jan 22, 2024

  1. Fix typo in comment.

    samsrabin authored Jan 22, 2024
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Commits on Jan 23, 2024

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  2. Merge remote-tracking branch 'adrifoster/interpMonthlyVeg_helper_func…

    …tion' into bfb_merge_tag_2315_et_al
    
    slevis resolved conflicts:
    src/main/clm_driver.F90
    slevis-lmwg committed Jan 23, 2024
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  3. Merge remote-tracking branch 'samsrabin/check-pyenv-FatesColdTwoStrea…

    …m' into bfb_merge_tag_2315_et_al
    slevis-lmwg committed Jan 23, 2024
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Commits on Jan 24, 2024

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  2. Revert "Merge remote-tracking branch 'adrifoster/interpMonthlyVeg_hel…

    …per_function' into bfb_merge_tag_2315_et_al"
    
    This reverts commit d327ec5, reversing
    changes made to 8189178.
    slevis-lmwg committed Jan 24, 2024
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Commits on Feb 1, 2024

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  2. Merge pull request ESCOMP#2342 from ESCOMP/fix-auto-assign

    Fix "Assign to project" Github action.
    samsrabin authored Feb 1, 2024
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  3. Merge pull request ESCOMP#2350 from samsrabin/fix-paramfile-format

    Delete history and spurious _FillValue from parameter files
    samsrabin authored Feb 8, 2024
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Commits on Feb 9, 2024

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Commits on Apr 1, 2024

  1. put in changes needed for addition of new dglc component

    Mariana Vertenstein committed Apr 1, 2024
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